clearai-dsh 0.3.0 → 0.4.0

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Files changed (148) hide show
  1. package/CHANGELOG.md +147 -0
  2. package/README.md +28 -28
  3. package/README.zh-CN.md +28 -28
  4. package/lib/client.js +861 -2555
  5. package/lib/domain-language.js +552 -48
  6. package/lib/fold.js +351 -1015
  7. package/lib/host.js +47 -557
  8. package/lib/invariant.js +9 -12
  9. package/lib/knowledge-view.js +363 -226
  10. package/lib/lang.js +81 -0
  11. package/package.json +1 -1
  12. package/presets/clearai/agent.cordis.yml +54 -82
  13. package/presets/clearai/clearai.patch.yml +54 -82
  14. package/presets/clearai/plugins/clearai-kernel.js +1590 -5437
  15. package/presets/clearai/plugins/ontology.js +56 -14
  16. package/presets/clearai/plugins/prompts.js +73 -363
  17. package/presets/clearai/skills/clearai-loop/SKILL.md +73 -59
  18. package/presets/clearai/plugins/brain.js +0 -547
  19. package/presets/clearai/plugins/commands.js +0 -199
  20. package/presets/clearai/template/knowledge/README.md +0 -25
  21. package/presets/clearai/template/memory/README.md +0 -34
  22. package/presets/clearai/template/project.md +0 -49
  23. package/presets/clearai/template/skills/README.md +0 -37
  24. package/presets/clearai/template/skills/chart-diagram-qa/SKILL.md +0 -43
  25. package/presets/clearai/template/skills/citation-management/SKILL.md +0 -73
  26. package/presets/clearai/template/skills/citation-management/references/bibtex_formatting.md +0 -908
  27. package/presets/clearai/template/skills/citation-management/references/citation_validation.md +0 -794
  28. package/presets/clearai/template/skills/citation-management/references/google_scholar_search.md +0 -725
  29. package/presets/clearai/template/skills/citation-management/references/metadata_extraction.md +0 -870
  30. package/presets/clearai/template/skills/citation-management/references/pubmed_search.md +0 -839
  31. package/presets/clearai/template/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  32. package/presets/clearai/template/skills/citation-management/scripts/extract_metadata.py +0 -569
  33. package/presets/clearai/template/skills/citation-management/scripts/format_bibtex.py +0 -349
  34. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic.py +0 -139
  35. package/presets/clearai/template/skills/citation-management/scripts/generate_schematic_ai.py +0 -817
  36. package/presets/clearai/template/skills/citation-management/scripts/search_google_scholar.py +0 -282
  37. package/presets/clearai/template/skills/citation-management/scripts/search_pubmed.py +0 -398
  38. package/presets/clearai/template/skills/citation-management/scripts/validate_citations.py +0 -497
  39. package/presets/clearai/template/skills/data-analysis/SKILL.md +0 -92
  40. package/presets/clearai/template/skills/data-analysis/checklists/readiness_check.md +0 -23
  41. package/presets/clearai/template/skills/data-analysis/templates/analysis_report.md.tpl +0 -63
  42. package/presets/clearai/template/skills/data-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -32
  43. package/presets/clearai/template/skills/data-analysis/templates/data_dictionary.md.tpl +0 -12
  44. package/presets/clearai/template/skills/data-analysis/templates/domain_knowledge_template.md.tpl +0 -316
  45. package/presets/clearai/template/skills/data-analysis/templates/feature_candidates.json.tpl +0 -20
  46. package/presets/clearai/template/skills/data-analysis/templates/quality_scorecard.md.tpl +0 -30
  47. package/presets/clearai/template/skills/data-analysis/workflows/01-data-profiling.md +0 -42
  48. package/presets/clearai/template/skills/data-analysis/workflows/02-quality-audit.md +0 -36
  49. package/presets/clearai/template/skills/data-analysis/workflows/03-physical-correlation.md +0 -25
  50. package/presets/clearai/template/skills/data-analysis/workflows/04-unstructured-mining.md +0 -26
  51. package/presets/clearai/template/skills/data-qa-analysis/SKILL.md +0 -102
  52. package/presets/clearai/template/skills/data-qa-analysis/checklists/readiness_check.md +0 -62
  53. package/presets/clearai/template/skills/data-qa-analysis/templates/best_in_class_report.md.tpl +0 -56
  54. package/presets/clearai/template/skills/data-qa-analysis/templates/cleaning_rules_draft.yaml.tpl +0 -56
  55. package/presets/clearai/template/skills/data-qa-analysis/templates/data_dictionary.md.tpl +0 -13
  56. package/presets/clearai/template/skills/data-qa-analysis/templates/data_source_inventory_and_lineage.md.tpl +0 -146
  57. package/presets/clearai/template/skills/data-qa-analysis/templates/data_status_report.md.tpl +0 -60
  58. package/presets/clearai/template/skills/data-qa-analysis/templates/steady_state_rules.yaml.tpl +0 -41
  59. package/presets/clearai/template/skills/data-qa-analysis/templates/subsystem_registry.md.tpl +0 -101
  60. package/presets/clearai/template/skills/data-qa-analysis/templates/unified_execution_plan.md.tpl +0 -100
  61. package/presets/clearai/template/skills/data-qa-analysis/workflows/01-data-source-inventory-and-lineage.md +0 -194
  62. package/presets/clearai/template/skills/data-qa-analysis/workflows/02-data-alignment-and-tag-semantics.md +0 -122
  63. package/presets/clearai/template/skills/data-qa-analysis/workflows/03-steady-state-identification.md +0 -126
  64. package/presets/clearai/template/skills/data-qa-analysis/workflows/04-consumption-analysis.md +0 -152
  65. package/presets/clearai/template/skills/data-qa-analysis/workflows/05-best-in-class-and-optimization-space.md +0 -78
  66. package/presets/clearai/template/skills/domain-presearch/SKILL.md +0 -131
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  68. package/presets/clearai/template/skills/domain-presearch/references/figure_code.md +0 -78
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  76. package/presets/clearai/template/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -517
  77. package/presets/clearai/template/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -633
  78. package/presets/clearai/template/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -547
  79. package/presets/clearai/template/skills/hypothesis-generation/SKILL.md +0 -73
  80. package/presets/clearai/template/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -329
  81. package/presets/clearai/template/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -198
  82. package/presets/clearai/template/skills/hypothesis-generation/references/literature_search_strategies.md +0 -622
  83. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic.py +0 -139
  84. package/presets/clearai/template/skills/hypothesis-generation/scripts/generate_schematic_ai.py +0 -817
  85. package/presets/clearai/template/skills/literature-review/SKILL.md +0 -72
  86. package/presets/clearai/template/skills/literature-review/references/citation_styles.md +0 -166
  87. package/presets/clearai/template/skills/literature-review/references/database_strategies.md +0 -455
  88. package/presets/clearai/template/skills/literature-review/scripts/generate_pdf.py +0 -176
  89. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic.py +0 -139
  90. package/presets/clearai/template/skills/literature-review/scripts/generate_schematic_ai.py +0 -817
  91. package/presets/clearai/template/skills/literature-review/scripts/search_databases.py +0 -303
  92. package/presets/clearai/template/skills/literature-review/scripts/verify_citations.py +0 -221
  93. package/presets/clearai/template/skills/paper-lookup/SKILL.md +0 -59
  94. package/presets/clearai/template/skills/paper-lookup/references/arxiv.md +0 -161
  95. package/presets/clearai/template/skills/paper-lookup/references/biorxiv.md +0 -118
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  102. package/presets/clearai/template/skills/paper-lookup/references/semantic-scholar.md +0 -203
  103. package/presets/clearai/template/skills/paper-lookup/references/unpaywall.md +0 -127
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  108. package/presets/clearai/template/skills/process-understanding-extraction/SKILL.md +0 -69
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  111. package/presets/clearai/template/skills/process-understanding-extraction/templates/entity_map_unit_topology.json.tpl +0 -86
  112. package/presets/clearai/template/skills/process-understanding-extraction/templates/process_brief.md.tpl +0 -89
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  115. package/presets/clearai/template/skills/process-understanding-extraction/templates/unified_execution_plan.md.tpl +0 -53
  116. package/presets/clearai/template/skills/process-understanding-extraction/workflows/01-process-doc-discovery.md +0 -173
  117. package/presets/clearai/template/skills/process-understanding-extraction/workflows/02-process-understanding-and-diagramming.md +0 -106
  118. package/presets/clearai/template/skills/scientific-brainstorming/SKILL.md +0 -64
  119. package/presets/clearai/template/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -326
  120. package/presets/clearai/template/skills/scientific-critical-thinking/SKILL.md +0 -72
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@@ -1,139 +0,0 @@
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- #!/usr/bin/env python3
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- """
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- Scientific schematic generation using Nano Banana 2.
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-
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- Generate any scientific diagram by describing it in natural language.
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- Nano Banana 2 handles everything automatically with smart iterative refinement.
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-
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- Smart iteration: Only regenerates if quality is below threshold for your document type.
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- Quality review: Uses Gemini 3.1 Pro Preview for professional scientific evaluation.
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-
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- Usage:
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- # Generate for journal paper (highest quality threshold)
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- python generate_schematic.py "CONSORT flowchart" -o flowchart.png --doc-type journal
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-
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- # Generate for presentation (lower threshold, faster)
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- python generate_schematic.py "Transformer architecture" -o transformer.png --doc-type presentation
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-
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- # Generate for poster
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- python generate_schematic.py "MAPK signaling pathway" -o pathway.png --doc-type poster
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- """
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-
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- import argparse
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- import os
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- import subprocess
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- import sys
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- from pathlib import Path
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-
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-
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- def main():
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- """Command-line interface."""
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- parser = argparse.ArgumentParser(
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- description="Generate scientific schematics using AI with smart iterative refinement",
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- formatter_class=argparse.RawDescriptionHelpFormatter,
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- epilog="""
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- How it works:
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- Simply describe your diagram in natural language
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- Nano Banana 2 generates it automatically with:
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- - Smart iteration (only regenerates if quality is below threshold)
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- - Quality review by Gemini 3.1 Pro Preview
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- - Document-type aware quality thresholds
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- - Publication-ready output
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-
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- Document Types (quality thresholds):
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- journal 8.5/10 - Nature, Science, peer-reviewed journals
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- conference 8.0/10 - Conference papers
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- thesis 8.0/10 - Dissertations, theses
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- grant 8.0/10 - Grant proposals
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- preprint 7.5/10 - arXiv, bioRxiv, etc.
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- report 7.5/10 - Technical reports
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- poster 7.0/10 - Academic posters
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- presentation 6.5/10 - Slides, talks
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- default 7.5/10 - General purpose
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-
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- Examples:
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- # Generate for journal paper (strict quality)
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- python generate_schematic.py "CONSORT participant flow" -o flowchart.png --doc-type journal
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-
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- # Generate for poster (moderate quality)
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- python generate_schematic.py "Transformer architecture" -o arch.png --doc-type poster
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-
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- # Generate for slides (faster, lower threshold)
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- python generate_schematic.py "System diagram" -o system.png --doc-type presentation
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-
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- # Custom max iterations
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- python generate_schematic.py "Complex pathway" -o pathway.png --iterations 2
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-
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- # Verbose output
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- python generate_schematic.py "Circuit diagram" -o circuit.png -v
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-
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- Environment Variables:
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- OPENROUTER_API_KEY Required for AI generation
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- """
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- )
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-
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- parser.add_argument("prompt",
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- help="Description of the diagram to generate")
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- parser.add_argument("-o", "--output", required=True,
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- help="Output file path")
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- parser.add_argument("--doc-type", default="default",
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- choices=["journal", "conference", "poster", "presentation",
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- "report", "grant", "thesis", "preprint", "default"],
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- help="Document type for quality threshold (default: default)")
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- parser.add_argument("--iterations", type=int, default=2,
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- help="Maximum refinement iterations (default: 2, max: 2)")
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- parser.add_argument("--api-key",
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- help="OpenRouter API key (or use OPENROUTER_API_KEY env var)")
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- parser.add_argument("-v", "--verbose", action="store_true",
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- help="Verbose output")
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-
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- args = parser.parse_args()
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-
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- # Check for API key
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- api_key = args.api_key or os.getenv("OPENROUTER_API_KEY")
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- if not api_key:
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- print("Error: OPENROUTER_API_KEY environment variable not set")
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- print("\nFor AI generation, you need an OpenRouter API key.")
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- print("Get one at: https://openrouter.ai/keys")
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- print("\nSet it with:")
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- print(" export OPENROUTER_API_KEY='your_api_key'")
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- print("\nOr use --api-key flag")
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- sys.exit(1)
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-
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- # Find AI generation script
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- script_dir = Path(__file__).parent
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- ai_script = script_dir / "generate_schematic_ai.py"
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-
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- if not ai_script.exists():
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- print(f"Error: AI generation script not found: {ai_script}")
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- sys.exit(1)
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-
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- # Build command
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- cmd = [sys.executable, str(ai_script), args.prompt, "-o", args.output]
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-
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- if args.doc_type != "default":
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- cmd.extend(["--doc-type", args.doc_type])
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-
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- # Enforce max 2 iterations
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- iterations = min(args.iterations, 2)
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- if iterations != 2:
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- cmd.extend(["--iterations", str(iterations)])
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-
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- if args.verbose:
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- cmd.append("-v")
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-
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- # Execute — pass API key via environment to avoid exposure in process listings
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- try:
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- env = os.environ.copy()
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- if api_key:
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- env["OPENROUTER_API_KEY"] = api_key
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- result = subprocess.run(cmd, check=False, env=env)
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- sys.exit(result.returncode)
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- except Exception as e:
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- print(f"Error executing AI generation: {e}")
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- sys.exit(1)
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-
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-
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- if __name__ == "__main__":
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- main()
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-